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SUEDE: a Strain-level UniquE DNA probE finder

Introduction

Pre-requests:

IMPORTANT: Do not use remote with blastn if you are using blast 2.9.0. This is a bug in blast -remote, will be fixed in blast 2.10.0. Blast nt database download instructions: https://www.ncbi.nlm.nih.gov/books/NBK537770/

Install commands

git clone https://gitlab.com/yileifu1996/probefinder.git
cd probefinder
./setup.sh

run example(please indicate nt database path if using blast 2.9.0)

python run.py -c example_control

Package explainations:

For genome download of Positive/Negative Group
ncbi-genome-download: https://github.com/kblin/ncbi-genome-download
For blastn
blast [there is a bug with -remote in blast 2.9.0, will be fixed in 2.10.0]
For unzip downloaded data
gunzip
For generating and exporting Tables and Heatmap
pandas: https://pandas.pydata.org/
seaborn: https://seaborn.pydata.org/
For getting Taxon ID from name, printing Newik Tree
ete3: http://etetoolkit.org/
Other Python Libraries
os, sys, argparse, numpy, progressbar
For getting MUMs
Parsnp: https://github.com/marbl/parsnp

Usage

usage: run.py [-h] [-w WORK_DIR] -c CONFIG_DIR -d DATABASE_PATH [-t]
          [-p PROCESSES] [-m]

SUEDE: Strain-level UniquE Dna probE finder

optional arguments:
-h, --help            show this help message and exit
-w WORK_DIR, --work_dir WORK_DIR
                        Directory of work directory, default: ../NCBITaxa/
-c CONFIG_DIR, --config_dir CONFIG_DIR
                        Directory of configuration file
-d DATABASE_PATH, --database_path DATABASE_PATH
                        Directory of NCBI nt database
-t, --tree_help       Use parsnp to generate a tree to evaluate positive
                        control? defalut: False
-p PROCESSES, --processes PROCESSES
                        Threads number, default: 70
-m, --MUMS_only       Only get MUMs, not blast against database? defalut:
                        False

First time running may take more time because ete3 will build a local taxa database.

Description

Pileline

Config File Explaination

bacteria

Mycobacterium tuberculosis

Mycobacterium bovis
Mycobacterium smegmatis
Mycobacterium avium
Mycobacterium kansasii
Mycobacterium fortuitum
Mycobacterium abscessus
  • The first Row is the Group that you want to get in NCBI Taxonomy Database
  • The second block is the Positive control
  • The third block is the Negative control